I was trying to run simulations in MCcoal using a file with heredity scalars but apparently there is a problem when reading this file. Is this option really possible? I would like to analyze the simulations with BP&P and I think this program does accept files with rates and heredity scalars.
thanks for the feedback
sincerely
arley
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The heredity scalar is available for the inference program bpp, but not the simulation program Mccoal. Mccoal does not allow different loci to have different scalars. You can write a small perl program to genarate tau and theta, wrote a mccoal control file, simulate each locus and then collect the different loci into one file.
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Anonymous
Anonymous
-
2013-04-15
Hi,
I am very beginner to learn about the BP&P software. I am wondering how can I make a file to run in the program and where I can see the output file. I run couple of example files in the software but the program is automatically cancelled while the run has showed he value to 100%. It will be really appreciated, if anybody can help me.
KK
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Anonymous
Anonymous
-
2013-06-06
You should run the program in a command line box (command-line terminal on mac or unix), and then you will see the output.
There are some notes about this at the paml web site, which you can look at.
ziheng yang
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
I was trying to run simulations in MCcoal using a file with heredity scalars but apparently there is a problem when reading this file. Is this option really possible? I would like to analyze the simulations with BP&P and I think this program does accept files with rates and heredity scalars.
thanks for the feedback
sincerely
arley
The heredity scalar is available for the inference program bpp, but not the simulation program Mccoal. Mccoal does not allow different loci to have different scalars. You can write a small perl program to genarate tau and theta, wrote a mccoal control file, simulate each locus and then collect the different loci into one file.
Hi,
I am very beginner to learn about the BP&P software. I am wondering how can I make a file to run in the program and where I can see the output file. I run couple of example files in the software but the program is automatically cancelled while the run has showed he value to 100%. It will be really appreciated, if anybody can help me.
KK
You should run the program in a command line box (command-line terminal on mac or unix), and then you will see the output.
There are some notes about this at the paml web site, which you can look at.
ziheng yang